Updated: Wed Dec 3 16:25:07 2014

DMR identification with methyl_diff

Background


UMR summary and sanity check

Sample Total.DMR Hyper.DMR Hypo.DMR
Cortex-HuFNSC02_Cortex-HuFNSC04 1283 179 1104
GE-HuFNSC02_GE-HuFNSC04 3002 722 2280

UMR asymmetry

GREAT enrichment for GW-associated UMRs

UMR Genomic breakdown

Proximal UMRs and DE genes

proximal.DMRs unique.genes DE.DMRs unique.DE.genes same.direction
Cortex04.UMRs 7 7 0 0 0
Cortex02.UMRs 215 215 24 19 21
GE04.UMRs 37 36 6 5 3
GE02.UMRs 402 402 64 57 49

Proximal 13-week UMRs in both Cortex and GE

id name description
ENSG00000189334 S100A14 S100_calcium_binding_protein_A14_[Source:HGNC_Symbol;Acc:18901]
ENSG00000237693 IRGM immunity-related_GTPase_family,M[Source:HGNC_Symbol;Acc:29597]
ENSG00000124564 SLC17A3 solute_carrier_family_17_(sodium_phosphate),member3_[Source:HGNC_Symbol;Acc:10931]

Proximal GE 13-week UMRs with DE genes

id name description DM DE
ENSG00000134954 ETS1 v-ets_erythroblastosis_virus_E26_oncogene_homolog_1_(avian)_[Source:HGNC_Symbol;Acc:3488] hyper UP
ENSG00000136352 NKX2-1 NK2_homeobox_1_[Source:HGNC_Symbol;Acc:11825] hyper UP
ENSG00000165588 OTX2 orthodenticle_homeobox_2_[Source:HGNC_Symbol;Acc:8522] hyper UP
ENSG00000231421 hyper DN
ENSG00000155760 FZD7 frizzled_family_receptor_7_[Source:HGNC_Symbol;Acc:4045] hyper DN

Proximal 17-week UMRs with DE genes in both Cortex and GE

id name description DM DE
ENSG00000255737 NA HCG2014417,isoformCRA_aUncharacterized_proteincDNA_FLJ59598_[Source:UniProtKB/TrEMBL;Acc:B7Z718] hypo UP
ENSG00000167178 ISLR2 immunoglobulin_superfamily_containing_leucine-rich_repeat_2_[Source:HGNC_Symbol;Acc:29286] hypo UP
ENSG00000161999 JMJD8 jumonji_domain_containing_8_[Source:HGNC_Symbol;Acc:14148] hypo UP
ENSG00000051523 CYBA cytochrome_b-245,alphapolypeptide_[Source:HGNC_Symbol;Acc:2577] hypo UP
ENSG00000169515 CCDC8 coiled-coil_domain_containing_8_[Source:HGNC_Symbol;Acc:25367] hypo UP
ENSG00000205927 OLIG2 oligodendrocyte_lineage_transcription_factor_2_[Source:HGNC_Symbol;Acc:9398] hypo UP
ENSG00000189060 H1F0 H1_histone_family,member0_[Source:HGNC_Symbol;Acc:4714] hypo UP
ENSG00000146904 EPHA1 EPH_receptor_A1_[Source:HGNC_Symbol;Acc:3385] hypo UP
ENSG00000165072 MAMDC2 MAM_domain_containing_2_[Source:HGNC_Symbol;Acc:23673] hypo UP

UMRs overlapping with TFBS

TF UMR17week_Cortex UMR13week_Cortex Ratio_Cortex UMR17week_GE UMR13week_GE Ratio_GE
MAZ 133 5 26.6000 319 12 26.5833
GTF2F1 28 1 28.0000 103 2 51.5000
ZBTB7A 97 3 32.3333 201 3 67.0000
HMGN3 66 2 33.0000 131 4 32.7500
NRF1 34 1 34.0000 64 1 64.0000
MXI1 112 3 37.3333 262 7 37.4286
E2F4 50 1 50.0000 110 1 110.0000
CCNT2 87 1 87.0000 148 4 37.0000
E2F6 140 1 140.0000 263 8 32.8750

UMR enrichment at chromosome ends

DE genes summary

UP DN DE
cortex01_cortex03 284 281 565
cortex01_cortex04 365 165 530
cortex02_cortex03 398 283 681
cortex02_cortex04 497 225 722
GE01_GE03 587 274 861
GE01_GE04 645 238 883
GE02_GE03 609 312 921
GE02_GE04 610 259 869

DAVID enrichment for DE genes

Isoform analysis

DE_genes DE_exons with_expressed_genes isoform_exons exclude_DE_genes isoform_genes
cortex01_cortex03 565 28637 16045 8044 7772 2490
cortex01_cortex04 530 27428 13200 6365 6134 2167
cortex02_cortex03 681 28963 16765 7961 7630 2425
cortex02_cortex04 722 29416 13894 6351 6011 2105
GE01_GE03 861 31361 14725 5880 5458 2041
GE01_GE04 883 34359 15889 6401 5996 2049
GE02_GE03 921 32827 15557 5773 5306 1965
GE02_GE04 869 34699 16012 6113 5711 1986